The Ocean Archive System searches our original datasets as they were submitted to us, not individual points or profiles. If you want to search and retrieve ocean profiles in a common format, or objectively analyzed fields, your better option may be to use one of our project applications. See: Access Data
OAS accession Detail for 0278593
| << previous | |revision: 2 |
| accessions_id: | 0278593 | archive |
|---|---|
| Title: | Microbial communities of corals analyzed using 454 Illumina pyrosequencing from Wonderland Reef, Florida in 2013 (NCEI Accession 0278593) |
| Abstract: | This dataset contains biological and survey - biological data collected at Caribbean_nearshore during deployment vanWoesik_2012 at Caribbean nearshore: Mahahual, Mexico; Tuxpan, Mexico; Robet van; St. John; Wonderland Reef, Florida from 2013-07-01 to 2013-08-31. These data include species and taxon. The instruments used to collect these data include Airbrush. These data were collected by Dr Robert van Woesik of Florida Institute of Technology as part of the "Are coral diseases contagious? (Contagious coral diseases?)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-06-11. The following is the text of the dataset description provided by BCO-DMO: Microbial communities of corals analyzed using 454 Illumina pyrosequencing Dataset Description: Coral disease transmission experiments were completed for dark-spot syndrome on Siderastrea siderea and yellow-band disease on Orbicella faveolata, as described in Randall et al. 2016. Following experimentation, microbial communities were extracted from tissue samples to determine whether any potential pathogen may have transmitted from healthy to exposed corals. Microbial communities on healthy corals were compared with diseased corals to identify any potential pathogens. Experimental diseased and healthy corals were sampled and their microbial communities were analyzed using 454 Illumina pyrosequencing of the amplified 16S rRNA gene on the V1-V3 hypervariable region. |
| Date received: | 20190611 |
| Start date: | 20130701 |
| End date: | 20130831 |
| Seanames: | |
| West boundary: | |
| East boundary: | |
| North boundary: | |
| South boundary: | |
| Observation types: | |
| Instrument types: | |
| Datatypes: | |
| Submitter: | |
| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
| Collecting institutions: | |
| Contributing projects: | |
| Platforms: | |
| Number of observations: | |
| Supplementary information: | Acquisition Description: [Adapted from: Randall et al. 2016] Immediately following completion of the waterborne-transmission experiments (See Randall et al. 2016), three each, of diseased, exposed, and healthy colonies of S. siderea were randomly selected for bacterial-community analyses, to determine whether potential bacterial pathogens had transmitted to the exposed colonies. The nine coral colonies were placed in individual, sterile whirl-paks at -80 degrees C and then were transported on dry ice to Mote Marine Laboratory in Sarasota, Florida. Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche airbrush with 10 mL of sterile seawater. The tissue slurry was collected in a sterile 50 mL Falcon® tube and homogenized using a vortex. The tissue homogenate was then spun down into a pellet using a centrifuge set at 10,000 rpm. The pellet was re-suspended in 2 mL of solution C1 and DNA was extracted using a Powersoil DNA extraction kit (MoBIO Laboratories Inc. Lot #PS14F19). Extracted DNA was then sent to MRDNA Laboratory (, Shallowater, TX, USA) for Illumina sequencing (20,000 reads per assay) using the universal bacterial primers 27F/519R with a barcode on the forward primer. The 16S rRNA gene on the V1 – V3 hypervariable region was amplified by applying a 30 cycle polymerase chain reaction (PCR) with the HotStarTaq Plus Master Mix Kit (Qiagen, USA). PCR was applied using the following protocol: (1) 94 degrees C for 3 minutes, (2) 28 cycles of: 94 degrees C for 30 seconds, 53 degrees C for 40 seconds, and 72 degrees C for 1 minute, and (3) a final elongation step at 72 degrees C for 5 minutes. After amplification, PCR products were confirmed in 2% agarose gels to determine the success of amplification and the relative intensity of the bands. Multiple samples were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads. Then the pooled and purified PCR product was used to prepare DNA libraries by following the Illumina TruSeq DNA library preparation protocol. Sequencing was performed using the Illumina sequencing platform at MR DNA (, Shallowater, TX, USA) following the manufacturer’s guidelines. Sequence data were processed using a standardized analysis pipeline. Briefly, sequences were initially depleted of barcodes. Then sequences less than 150bp or with ambiguous base calls were removed. Operational taxonomic units (OTUs) were generated, and chimeras were removed using UCHIME [48]. OTUs were defined by clustering at 3% divergence (i.e., showing 97% similarity) using a de novo method. Final OTUs were taxonomically classified using BLASTn against the curated National Center for Biotechnology Information (NCBI) database and the Ribosomal Database Project (RDP). Field collection: Wonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013. Laboratory experimentation: Mote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida from 10 July – 14 August 2013. |
| Availability date: | |
| Metadata version: | 2 |
| Keydate: | 2023-05-22 04:18:41+00 |
| Editdate: | 2024-04-19 13:13:41+00 |